Can modifiers be computed and applied from the command line?
You'd have to use bpy.ops.object.modifier_apply, e.g.

import bpy

for obj in bpy.context.scene.objects:
    bpy.context.scene.objects.active = obj
    count = 1
    length = len(obj.modifiers)
    while obj.modifiers:
        name = obj.modifiers[0].name
        print("%s: Applying %s (%d/%d)" % (obj, name, count, length))
        bpy.ops.object.modifier_apply(modifier=name)
        count += 1
print("All done.")


For info on how to to run the above, see here.